Swab Types Research Articles

Effect of different types of dry swabs and their storage conditions on the inoculation of Corynebacterium diphtheriae.

The results of evaluating the effectiveness of C. diphtheriae inoculation using different types of dry swabs in studies simulating various conditions of its storage at the preanalytical stage of a laboratory study for diphtheria are presented. A typical toxigenic strain of C. diphtheriae biovar gravis No. 665 was used. A commercial dry, sterile cotton swab probe (Ningbo Greetmed Medical Instruments Co., LTD, China), a commercial dry, sterile swab probe (plastic and viscose) (COPAN, Italy), tufters with a fluffy probe-tampon on a polystyrene applicator, standard (DELTALAB, SL, Spain). The tampons were pooled with a 24-hour bacterial culture of C. diphtheriae, then immediately seeded on Tellurite-containing blood agar and Corynebacagar. Storage conditions were simulated for 3 hours: at room conditions +(20-25)°C, in the refrigerator +(4-8)°C, in a thermostat +(37±1)°C. Optimal storage of C. diphtheriae on all three types of dry swabs at + (4-8) ° C; at +(20-25)° C - growth is observed when seeding from a cotton swab; in a swab with a fleecy probe-tampon, a decrease in the inoculation of C. diphtheriae was noted; when using a viscose swab - a significant loss of C. diphtheriae. At +(37±1)°C, a significant decrease in the inoculation of C. diphtheriae on all three types of tampons was noted, up to the absence of growth when using a viscose tampon. To exclude the loss of C. diphtheriae, it is necessary to observe the conditions for taking and storing biological material at the preanalytical stage of a laboratory study, which will improve the quality of laboratory microbiological studies for diphtheria infection.

Collaborative swab performance comparison and the impact of sampling solution volumes on DNA recovery

The collection of DNA traces marks the first step determining the success of genetic analysis. This study aimed to identify and validate a suitable alternative to the currently used ForensiX Evidence Collection Kit containing a cardboard box for swab storage. This box has to be folded at the crime scene, which is time-consuming and carries the risk of potential contamination and handling difficulties.A collaboration study involving three police departments and one laboratory for forensic genetics was performed to compare the currently used swab against three challenger swabs: ForensiX SafeDry, Copan 4N6FLOQSwab™ Genetics and Copan 4N6FLOQSwab™ Crime Scene. Mock samples consisted mainly of touch DNA, but also blood, saliva and semen were applied to twelve items with different surfaces. Every organisation contributed with three DNA collectors, whose individual collection efficiencies were investigated. The challenge of preparing homogenous traces, especially touch DNA, was addressed by enhancing hand contact frequency and sampling area. As a further part of the swab comparison study, we describe for the first time the influence of different swabbing solution volumes on the sampling efficiency of the different swabs.The application of touch DNA was also tested for a further swab type, the Sarstedt Forensic Swab, which yielded such low DNA concentrations that it was excluded from the collaboration study. The Copan Genetics and Copan Crime Scene swabs yielded significantly lower DNA concentrations than the currently used ForensiX Evidence Collection Kit and ForensiX SafeDry swab. The inter-individual performance results of the operators revealed significant differences in sampling skills. Comparing different swabbing solution volumes showed higher DNA yields or no significant difference for the ForensiX Evidence Collection Kit and ForensiX SafeDry than the Copan Genetics, depending on the item or trace type swabbed.Our results highlight the importance of validating first-step components that are decisive to the success of DNA typing in the context of specific sampling procedures and laboratory methods. Also, the significance of individuals' securing variations, principally unknown for crime scene investigation and laboratory teams, is emphasised for the first time, offering a practical approach for improving and training DNA collecting activities and ensuring the optimal securing evidence process. These findings increase the knowledge of impacts on DNA collection and, thus, benefit other laboratories and forensic services, particularly when using the same extraction methods.

The effect of NucleoSpin® Forensic Filters on DNA recovery from trace DNA swabs

Forensic DNA profiling is a globally accepted method for human identification, however, obtaining full DNA profiles from trace DNA can be challenging. The optimal recovery of DNA from trace DNA swabs is therefore crucial. Methods for extracting DNA from swabs often make use of a spin basket combined with a centrifugation step, to enhance the release of cells from the swab prior to DNA extraction. The NucleoSpin® Forensic Filter (Macherey-Nagel, Düren) is a type of spin basket, but it has not been thoroughly assessed on trace DNA samples. This study aimed to assess if the inclusion of the NucleoSpin® Forensic Filter significantly improved DNA recovery and DNA profiling success from cotton and flocked swabs used to collect trace DNA and buccal cells (control). Buccal cells and trace DNA samples were collected from 25 volunteers using each swab type (cotton and flocked) in duplicate. DNA was extracted from the samples using the NucleoSpin® DNA Forensic kit, one set with, and the other set without, NucleoSpin® Forensic Filters. DNA concentration was assessed using real time PCR, and DNA profiling was done using the PowerPlex® ESX 16 system. The inclusion of the NucleoSpin® Forensic Filters significantly improved DNA concentration for buccal cells that were collected using flocked swabs (p = 0.035). However, no significant differences were noted for trace DNA samples for either swab type. There was also no significant difference in DNA profiling success when NucleoSpin® Forensic Filters were used, regardless of swab and sample type. These results may be helpful for laboratories that are considering the NucleoSpin® Forensic Filters in the DNA extraction workflow, particularly for trace DNA samples.

Development of a Microneedle Swab for Acquisition of Genomic DNA From Buccal Cells.

A swab is a tool for obtaining buccal DNA from buccal mucus for biological analysis. The acquisition of a sufficient amount and high quality of DNA is an important factor in determining the accuracy of a diagnosis. A microneedle swab (MN swab) was developed to obtain more oral mucosal tissues non-invasively. Eight types of MN swabs were prepared with varying combinations of patterns (zigzag or straight), number of MNs, intervals of MNs, and sharpness of tips. When MN swab was applied up to 10 times, the tissue amount and DNA yield increased compared to commercial swabs. A zigzag pattern of microneedles was found to be more efficient than a straight pattern and increasing the number of microneedles in an array increased the DNA yield. The MN swab collected about twice the DNA compared to the commercial swab. In an in vivo test using mini pigs, the lower cycle threshold values of mucosal samples collected with MN swabs compared to samples collected with commercial swabs indicated that a greater amount of DNA was collected for SNP genotyping. A polymer MN swab is easy to manufacture by a single molding process, and it has a greater sampling capacity than existing commercial swabs.

Performance of anterior nares and tongue swabs for nucleic acid, Nucleocapsid, and Spike antigen testing for detecting SARS-CoV-2 against nasopharyngeal PCR and viral culture

ObjectivesThis study assesses and compares the performance of different swab types and specimen collection sites for SARS-CoV-2 testing, to reference standard real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and viral culture. MethodsSymptomatic adults with COVID-19 who visited routine COVID-19 testing sites used spun polyester and FLOQSwabs to self-collect specimens from the anterior nares and tongue. We evaluated the self-collected specimen from anterior nares and tongue swabs for the nucleocapsid (N) or spike (S) antigen of SARS-CoV-2 by RT-PCR and then compared these results with results from RT-PCR and viral cultures from nurse-collected nasopharyngeal swabs. ResultsDiagnostic sensitivity was highest for RT-PCR testing conducted using specimens from the anterior nares collected on FLOQSwabs (84%; 95% CI 68-94%) and spun polyester swabs (82%; 95% CI 66-92%), compared to RT-PCR tests conducted using specimens from nasopharyngeal swabs. Relative to viral culture from nasopharyngeal swabs, diagnostic sensitivities were higher for RT-PCR and antigen testing of anterior nares swabs (91-100%) than that of tongue swabs (18-81%). Antigen testing of anterior nares swabs had higher sensitivities against viral culture (91%) than against nasopharyngeal RT-PCR (38-70%). All investigational tests had high specificity compared with nasopharyngeal RT-PCR. Spun polyester swabs are equally effective as FLOQSwabs for anterior nasal RT-PCR testing. ConclusionsWe found that anterior nares specimens were more sensitive than tongue swab specimens or antigen testing for detecting SARS-CoV-2 by RT-PCR. Thus, self-collected anterior nares specimens may represent an alternative method for diagnostic SARS-CoV-2 testing in some settings.

Screening for cytomegalovirus shedding in vagina and saliva: Significant differences between biological fluids, swab types and storage durations in DNA recovery.

Cytomegalovirus (CMV) shedding in genital and oral secretions during pregnancy is associated with adverse outcomes. Sample collection methods between studies are not uniform and currently there are limited data on the impact of biological fluids, swab types and storage durations on the detection of CMV DNA. To evaluate the absorption efficiency and CMV DNA recovery of various commercially available swabs in vaginal and saliva fluids. The absorption volume of different swab types was evaluated. The recovery of CMV DNA over time from vaginal and saliva fluids, and vaginal and saliva swabs, was evaluated by PCR measurements of samples spiked with CMV standard. Absorption efficiency of swabs varied significantly. The duration of storage did not affect CMV DNA recovery from vaginal fluid or swabs, but did significantly affect CMV DNA recovery from neat saliva fluid and saliva swabs stored dry or in viral transport media (VTM). Flocked swab/eNAT media recovered the highest amount of CMV DNA from both fluids. In saliva, flocked swab/eNAT media and polyester swab/cobas media demonstrated a higher CMV DNA recovery than foam swab/VTM. 25% of dry saliva foam swabs were falsely negative for CMV DNA. Recovery of CMV DNA is dependent on sample type and swab type used. Flocked swab/eNAT media and polyester swab/cobas media appear acceptable, though flocked swab/eNAT media was superior demonstrating the best recovery of CMV DNA. For saliva, foam swabs stored dry or in VTM was shown to be inferior to flocked or polyester swabs.

Anatomical Site, Viral Ribonucleic Acid Abundance, and Time of Sampling Correlate With Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2 During Infection

BackgroundNasopharyngeal (NP) swabs are the standard for SARS-CoV-2 diagnosis. If less invasive alternatives to NP swabs (eg, oropharyngeal [OP] or nasal swabs [NS]) are comparably sensitive, the use of these techniques may be preferable in terms of comfort, convenience, and safety. MethodsThis study compared the detection of SARS-CoV-2 in swab samples collected on the same day among participants with at least one positive PCR test. ResultsOverall, 755 participants had at least one set of paired swabs. Concordance between NP and other swab types was 75% (NS), 72% (OP), 54% (rectal swabs [RS]), and 78% (NS/OP combined). Kappa values were moderate for the NS, OP, and NS/OP comparisons (0.50, 0.45, and 0.54, respectively). Highest sensitivity relative to NP (0.87) was observed with a combination of NS/OP tests (positive if either NS or OP was positive). Sensitivity of the non-NP swab types was highest in the first week postsymptom onset and decreased thereafter. Similarly, virus RNA quantity was highest in the NP swabs as compared with NS, OP, and RS within two weeks postsymptom onset. OP and NS performance decreased as virus RNA quantity decreased. No differences were noted between NS specimens collected at home or in clinic.ConclusionsNP swabs detected more SARS-CoV-2 cases than non-NP swabs, and the sensitivity of the non-NP swabs decreased with time postsymptom onset. While other swabs may be simpler to collect, NP swabs present the best chance of detecting SARS-CoV-2 RNA, which is essential for clinical care as well as genomic surveillance.

Sampling Methods and Risk Stratification Regarding Environmental Contamination by SARS-CoV-2.

Transmission of COVID-19 through close contact and droplets is well established, but the influence of aerosol and surface contamination remains to be determined. Literature is scarce and inconsistent about the viable virus particles free-distance from infected patients, as well as about different swabbing methods for surface contamination evaluation. The aim of this study was to evaluate the most sensitive method for the assessment of surface contamination, classify the likelihood of environmental contamination in risk zones and compare the environmental contamination between oxygenation and ventilatory support. Swabs from potentially contaminated surfaces in a COVID-19 ward, with patients treated with different types of oxygen and ventilatory support, were collected. Three types of swabs were compared in order to evaluate the most sensitive collection method. For risk zone categorization, areas were divided according to the distance from the patient. Of the 63 swabs collected, 17 (27%) tested positive for the presence of SARS-CoV-2. The highest positivity rate was observed with the sterile premoistened swab with saline (n = 8; 38%), but without statistically significant differences. The highest number of positive samples were collected from the high-risk zones, specifically those located one meter from the patient (n = 13; 48%), with statistically significant differences. Only the rooms of patients supported with non-invasive ventilation or high-flow nasal cannula had evidence of bedroom contamination, with 45% and 27% of swab positivity, with statistically significant differences. Our findings favour the premoistened swab without transport medium for surface contamination assessment, even though without statistical differences. A statistically significant trend supporting the division in risk zones, according to the distance from the patient, was also identified. The higher positivity rate from the non-invasive ventilation and high-flow nasal cannula bedrooms suggests a significant association between ventilatory strategies and surface contamination, probably due to higher particle dispersion. Our findings support the use of the sterile premoistened swab without preservation medium, the classification of risk areas considering the distance from the patient, and the variability of RNA dispersion between oxygenation and ventilatory support.

Touch DNA recovery from vehicle surfaces using different swabs.

Several methods of DNA collection are used in places or objects related to crimes, the most common being the use of swabs. However, it is known that the efficacy of touch DNA recovery can be affected by collection devices and surfaces. The aim of this work was to evaluate the efficiency of three different types of swab in recovering touch DNA collected from different parts of a vehicle. The following swabs were tested: PurFlock® swab (Puritan, USA), 4N6FLOQSwabs™ (Copan S.p.A., Italy), and cotton swab (Labor Import). The experiments were carried out in the same vehicle, using the gearshift knob, the parking brake lever, and the steering wheel as support for the collection of touch DNA. Swabs showed significant differences in the amount of DNA recovered (Hc = 53.52; p < 0.05) and in the rate of allele amplification (Hc = 24.3; p < 0.05). The results indicated a greater DNA recovery efficiency by PurFlock® swab, followed by cotton, and then 4N6FLOQSwabs™. However, there was no significant difference among the surfaces analyzed. PurFlock® swab was more efficient for recovering donor alleles than the others (cotton and 4N6FLOQSwabs™), especially for small DNA amounts. This swab was, therefore, suitable for collections in vehicles involved in crime. Furthermore, this study highlights the need to assess different materials and methods of collection of biological samples, considering collection, extraction, and amplification.

Morphological characteristics of X-ray thorax images of COVID-19 patients using the Bradley thresholding segmentation

The coronavirus disease 2019 (COVID-19) pandemic has made test screening much needed. Currently, the most commonly used is the swab type. Although in fact, there is also a screening method with chest radiology. The purpose of this study is to develop a COVID-19 early detection system based on X-ray images of the patient's thorax in the form of a computer-aided diagnosis. This case is based on the fact that X-ray modalities are available in several health care centers in Indonesia, compared to other modalities such as computed tomography (CT) scan or magnetic resonance imaging (MRI). In this paper, we emphasize the X-ray thorax image segmentation process to explore the morphological information of the thorax. We use the Bradley thresholding segmentation method. The results obtained are promising to be further developed with a performance percentage of 73.33% for the thorax for COVID-19 patients and 54% for the thorax for normal patients.

An algorithmic approach to the use of rapid molecular diagnostics for SARS-CoV-2, influenza viruses, and other respiratory pathogens during an unprecedented respiratory season

Abstract Introduction/Objective The COVID-19 pandemic exacerbated deficiencies of testing personnel, reagents, supplies and disposables, instruments, and automation in many clinical laboratories. Upon entering respiratory season, a strategy was warranted to optimize laboratory resources when supplies were already limited and expected respiratory season test volume was unknown. An algorithm was devised to prioritize test ordering and TAT based on patient clinical scenario. Methods/Case Report The institutional respiratory season SARS-CoV-2 algorithm was constructed by a multidisciplinary team including infectious disease, infection prevention, laboratory, and IT/LIS leadership. CDC guidance on influenza testing was incorporated. Antigen-based testing was discontinued; only molecular amplification- based platforms with FDA EUA were utilized. Platforms had a range of TAT (20 minutes to 8 hours) and included fully- automated high throughput, rapid random access, point-of-care, and CDC SARS-CoV-2 assays. Test bundles included SARS-CoV-2 (monoplex), or SARS-CoV-2 + fluA&amp;B (triplex), or SARS-CoV-2 + respiratory pathogen panel (multiplex RPP; includes 22 targets, including flu A&amp;B). Results (if a Case Study enter NA) Key factors in the algorithm included whether the patient was outpatient or inpatient, hospital employee or not, symptomatic or not, immunocompetent or immunocompromised, and whether a concurrent order for other respiratory pathogens was included or not. Clinician responses for these factors determined the type of swab collected (wet swab in VTM or dry swab) and how quickly the TAT was indicated for a given patient using a colored-dot sticker system. Priority TAT in decreasing order was symptomatic inpatients, asymptomatic pre- procedure patients, asymptomatic admissions, symptomatic employees, and symptomatic outpatients. Conclusion An algorithm for respiratory pathogen testing during an unprecedented respiratory season prioritizes result TAT to an individual patient’s clinical situation while maximizing laboratory stewardship by eliminating redundant influenza testing and requiring ‘all upfront’ orders to avoid add-on orders that require ‘dumpster diving’ for samples. Limitations include inherent differences in sensitivity, LOD, and specificity when multiple different platforms are utilized to detect the same analytes.

The Ocular Microbiome Is Altered by Sampling Modality and Age.

BackgroundStudies of the ocular microbiome have used a variety of sampling techniques, but no study has directly compared different sampling methods applied to the same eyes to one another or to a reference standard of corneal epithelial biopsy. We addressed this lack by comparing the microbiome from three conjunctival swabs with those of corneal epithelial biopsy.MethodsTwelve eyes (11 patients) were swabbed by calcium alginate swab, cotton-tipped applicator, and Weck-Cel cellulose sponge before a corneal epithelial biopsy (48 samples). We then performed 16S rRNA gene sequencing and universal 16S rRNA gene real-time polymerase chain reaction. Negative/blank controls were used to eliminate contaminants. An analysis was performed to examine the concordance of the three swab types to corneal epithelial biopsy. The effect of patient age on the ocular microbiome as determined by epithelial biopsy was also examined.ResultsThe ocular microbiome from corneal epithelial biopsies consisted of 31 genera with a relative abundance of 1% or more, including Weisella, Corynebacterium, and Pseudomonas. Of the three swab types, Weck-Cel differed the most from corneal biopsies based on beta-diversity analysis. Cotton swabs were unable to capture the Bacteroides population seen on epithelial biopsy. Therefore, calcium alginate swabs seemed to be the closest to epithelial biopsies. Older patients (≥65 years old) had higher alpha diversity (P < 0.05) than younger patients. Differential abundance testing showed that there were 18 genera that were differentially abundant between the two age groups, including Streptococcus and eight members of the Proteobacteria phylum.ConclusionsWe demonstrate that ocular sampling method and patient age can greatly affect the outcome of sequencing-based analysis of the ocular microbiome.Translational RelevanceBy understanding the impact of different sampling methods on the results obtained from the ocular surface microbiome, future research on the topic will be more reproducible, leading to a better understanding of ocular surface microbiome in health and disease.

Collection and storage of DVI samples with microFLOQ® Direct swabs for direct amplification

The rapid identification of decomposing human remains is a crucial component of disaster victim identification (DVI), often occurring in remote areas without access to laboratory or storage facilities. Due to the ease of collection and amenability to storage in harsh conditions, swabs may be used to collect DNA from decomposing remains as an alternative to sampling tissue or bone. Direct amplification could further streamline the process and reduce costs. This study investigated the efficacy of direct amplification of DVI samples using microFLOQ® Direct swabs and the QIAGEN Investigator QS GO! Kit. A comparison of performance between direct amplification and traditional methods was made to assess whether direct amplification offered an improvement to traditional methods. DNA was collected by swabbing the muscle of a decomposing human cadaver using three swab types (ADS Genetics 4N6FLOQSwabs®, NADS Genetics 4N6FLOQSwabs®, and the microFLOQ® Direct swab). Traditional swabs (4N6FLOQSwabs®) were extracted and quantified, while a direct amplification strategy was used with the microFLOQ® Direct swabs coupled with the Investigator 24Plex GO! Kit. Processing of the microFLOQ® Direct swabs were optimized and a hybrid strategy that used 4N6FLOQSwabs® to collect and store DNA before swabbing or “subsampling” the 4N6FLOQSwabs® for processing with microFLOQ® Direct swabs was developed. This hybrid strategy allowed for rapid processing without the consumption of the original sample. Traditional and direct PCR methods were comparable up to day 10 of decomposition depending on the sample location and for up to 3 months of storage at room temperature. This research indicated that microFLOQ® Direct swabs in conjunction with the Investigator 24Plex GO! Kit can be used to facilitate rapid direct processing of DNA from decomposing human remains.

Relative sensitivity of anterior nares and nasopharyngeal swabs for initial detection of SARS-CoV-2 in ambulatory patients: Rapid review and meta-analysis.

Nasopharyngeal (NP) swabs are considered “gold standard” for diagnosing SARS-CoV-2 infections, but anterior nares or mid-turbinate swabs (nasal swabs) are often used. We performed a meta-analysis comparing the sensitivity of nasal and nasopharyngeal swabs against a composite reference standard for the initial diagnosis of SARS-CoV-2 infection in ambulatory patients. The study is registered on PROSPERO (CRD42020221827). Data sources included studies appearing between January 1, 2020 and March 20, 2021, identified by searches of PubMed, medRxiv and bioRxiv. Studies included at least 20 subjects who simultaneously provided nasal and nasopharyngeal specimens for reverse transcription-polymerase chain reaction testing, and for which confusion matrices could be constructed. Authors individually assessed studies for inclusion and compared assessments. Each author independently extracted all data elements; differences were reconciled by review of initial data sources. Extracted data included specimen site, patient characteristics, collection site, and confusion matrices comparing results for nasal and nasopharyngeal swabs. Assessed against a composite reference standard, anterior nares swabs are less sensitive (82% - 88%) than nasopharyngeal swabs (98%). For populations with 10% specimen positivity, the negative predictive values of all swab types were greater than 98%. Mid-turbinate and anterior nares swabs seem to perform similarly. The lower sensitivity associated with nasal swab SARS-CoV-2 diagnosis is justified by the ability to screen more patients and reduced personal protective equipment requirements. Our conclusions are limited by the small number of studies and the significant heterogeneity of study designs and study outcomes.

Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19.

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including “RT-PCR or viral load”, “SARS-CoV-2 and RT-PCR”, “Ct value and viral load”, “Ct value or COVID-19”. Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

Accuracy of the Mologic COVID-19 rapid antigen test: a prospective multi-centre analytical and clinical evaluation

Background: The coronavirus disease 2019 (COVID-19) pandemic has highlighted the reliance on antigen detection rapid diagnostic tests (Ag-RDTs). Their evaluation at point of use is a priority. Methods: Here, we report a multi-centre evaluation of the analytical sensitivity, specificity, and clinical accuracy of the Mologic COVID-19 Ag-RDT by comparing to reverse transcriptase polymerase chain reaction (RT-qPCR) results from individuals with and without COVID-19 symptoms. Participants had attended hospitals in Merseyside, hospital and ambulance services in Yorkshire, and drive-through testing facilities in Northumberland, UK. Results: The limit of detection of the Mologic COVID-19 Ag-RDT was 5.0 x 102 pfu/ml in swab matrix with no cross-reactivity and interference for any other pathogens tested. A total of 347 participants were enrolled from 26th of November 2020 to 15th of February 2021 with 39.2% (CI 34.0-44.6) testing RT-qPCR positive for SARS-CoV-2. The overall sensitivity and specificity of the Mologic Ag-RDT compared to the reference SARS-CoV-2 RT-qPCR were 85.0% (95% CI 78.3-90.2) and 97.8% (95.0-99.3), respectively. Sensitivity was stratified by RT-qPCR cycle threshold (Ct) and 98.4% (91.3-100) of samples with a Ct less than 20 and 93.2% (86.5-97.2) of samples with a Ct less than 25 were detected using the Ag-RDT. Clinical accuracy was stratified by sampling strategy, swab type and clinical presentation. Mologic COVID-19 Ag-RDT demonstrated highest sensitivity with nose/throat swabs compared with throat or nose swabs alone; however, the differences were not statistically significant. Conclusions: Overall, the Mologic test had high diagnostic accuracy across multiple different settings, different demographics, and on self-collected swab specimens. These findings suggest the Mologic rapid antigen test may be deployed effectively across a range of use settings.

Suitability of specific soft tissue swabs for the forensic identification of highly decomposed bodies

When decomposition of a recovered body is fairly advanced, identification based on common morphologic features is often impossible. In these cases, short tandem repeat (STR) marker genotyping has established itself as a convenient and reliable alternative. However, at very progressed stages of decomposition, postmortem tissue putrefaction processes can decrease DNA yields considerably. Hence, not all types of tissue are equally suitable for successful STR marker-based postmortem identification. Bone or dental material is often analysed in corpses with advanced decompositional changes. However, processing of these materials is very elaborate and time and resource consuming. We have therefore focused on the suitableness of various types of soft tissue swabs, where DNA extraction is easier and faster. By sampling 28 bodies at various stages of decomposition, we evaluated the suitability of different tissues for genotyping at varying degrees of physical decay. This was achieved by a systematic classification of the sampled bodies by morphological scoring and subsequent analysis of multiple tissue swabs of the aortic wall, urinary bladder wall, brain, liver, oral mucosa and skeletal muscle. In summary, we found variable degrees of suitability of different types of soft tissue swabs for DNA-based identification. Swabs of the aortic wall, the urinary bladder wall and brain tissue yielded the best results — in descending order — even at advanced levels of decay.

Enhanced forensic DNA recovery with appropriate swabs and optimized swabbing technique

Efficient sampling with swabs is crucial for optimal forensic DNA analysis. The DNA recovery is determined by the skill of the practitioner and the compatibility between the applied swab and the surface. Here we investigate the impact of swabbing technique and swab type on the DNA yield. Thirteen different swabs from four categories (cotton, flocked nylon, small foam and large foam) provided equal DNA yields for smooth/non-absorbing surfaces. Large foam swabs gave higher DNA recovery for an absorbing wood surface. Factorial design of experiments and ANOVA was applied to study swabbing techniques for cotton swabs. Two key factors for efficient sampling were found to be 1) holding the swab with an approximate 60° angle against the surface and 2) to rotate the swab during sampling. For absorbing wood, it was beneficial to wet the swab heavily. The results of the factorial experiments were used to develop swabbing protocols for different surfaces. When ten experienced practitioners sampled according to these protocols, the DNA yield was increased for ridged plastic (around 1.25 times more DNA) and absorbing wood (2.2–6.2 times more DNA). For window glass, representing a smooth/non-absorbing surface, sampling according to the protocol gave DNA yields equivalent to applying individual sampling techniques. The protocol lowered person-to-person variation for ridged plastic. In conclusion, we have developed instructive protocols for cotton swab sampling on three types of surfaces: smooth/non-absorbing, ridged/non-absorbing and smooth/absorbing. We believe that such swabbing protocols will streamline and simplify the training of new practitioners and improve sampling efficiency for invisible DNA residues in casework.

Comparison of the sensitivity of the Gene-Up® and ANSR Listeria Right NowTM assays and the influence of swab type when detecting Listeria monocytogenes in the environment with a dairy context

This study tested the Gene-Up® protocol for Listeria and the Listeria Right Now™ environmental test for their abilities to detect dairy-related Listeria monocytogenes when present on stainless steel surfaces. Different swabbing materials were tested to evaluate whether they affected the detection capability of these methods. The swab used in the ANSR Listeria Right Now™ assay recovered 2% of L. monocytogenes inoculated on a surface, while other swabs recovered up to 10%. The ANSR Listeria Right Now™ assay detected 1 cfu, and the Gene-Up® method detected 10 cfu of L. monocytogenes when media was directly inoculated (without using swabs). When swabs were used the sensitivities of both assays were similar. This study showed that both the recovery percentage of L. monocytogenes from surfaces by swabs and the in-assay sensitivity contribute toward the overall sensitivity of methods used to detect L. monocytogenes from surfaces in the dairy context.

Identification of diverse novel genomoviruses in gut of wild birds

Genomoviridae is a virus family belonging to circular replication associated protein encoding ssDNA (CRESS-DNA) viruses, which have diverse genomic architecture and are widely distributed among different ecosystems. In this study, we characterized 39 novel genomovirus genomes including 3 from wild egrets, 9 from wild cranes, as well as 27 from wild finches in three different types of cloacal swabs of wild bird sampled in the station of Xinqing bird ringing, Maoershan Nature Reserve in Heilongjiang Province, Changbai Mountain in Jilin Province, and Hangzhou Wetland Park in Zhejiang Province, China. Here, using a Rep sequence phylogeny-based analysis, we divided the 39 genomoviruses into 8 genera within the family Genomoviridae, including Gemycircularvirus (n=20), Gemykibivirus (n=3), Gemygorvirus (n=2), Gemyvongvirus (n=2), Gemykolovirus (n=3), Gemykrogvirus (n=6), Gemytondvirus (n=1), Gemyduguivirus (n=1) and one unclassified genomovirus. The 39 genomovirus genomes belong to 36 species (27 of which are new) based on the currently accepted genomovirus pairwise nucleotide sequence identity species demarcation threshold of 78%. Overall, the research enriches our knowledge of CRESS-DNA viral diversity in China and emphasizes the prevalence of genomoviruses in nature.